But human flesh was too frail, too paltry to hold the terrific essence that was Khosatral Khel. So he stood up in the shape and aspect of a man, but his flesh was not flesh; nor the bone, bone; nor blood, blood. He became a blasphemy against all nature, for he caused to live and think and act a basic substance that before had never known the pulse and stir of animate being.
In Haruhi Suzumiya, Kuyou Suou / Suou Kuyou (the proper order is purposefully left unknown). While the other Humanoid Interfaces are weird, Kuyou is described by the narration as simply wrong. Her ordinary movements like walking seem to defy the laws of physics in inexplicable ways, and her words and motivations are even less comprehensible than the others. Kyon is terrified to simply be in her presence.
The Mad God Asura from Soul Eater is still recognizably human in appearance... but his mere unsealing creates a wave of insanity that critically weakens the good guys while creating new enemies and empowering existing ones.
As of ch72, this seems to be the case for Death the Kid being a 'fragment' of one of the Great Old Ones, i.e Shinigami. The Index refers to him as part of the "madness of the rule of law" which would fit. Asura claims that he is also a 'fragment' of Shinigami, making him Kid's older brother.
In Apocalypse No Toride (Fortress of The Apocalypse) the four juvenile delinquents escape from prison (which has been overrun with zombies) into the city and encounter a giant mountain of rotting zombies controlled by an androgynous naked man on the top, using the zombies like a grotesque throne. When Maeda catches its attention, said naked man (who was about a half-mile away) uses the zombies to move like a hideous organism at lightening speed, until it's only a foot in front of the terrified youth. A close-up reveals that it has Sharingan-like eyes, with three smaller eyes inhabiting each of its pupils.
Neon Genesis Evangelion has Rei and Kaworu, who are the soul (or part of a soul) of an Angel jammed into a soulless clone body, and are even more powerful and just as incomprehensible as the "regular" Angels.
Baccano! has Ronnie Schiatto, an ancient and incomprehensibly powerful "demon" who decided to take human form and become a gangster for the lulz. While he's usually content to just sit back and be the All-Powerful Bystander, sometimes he likes to switch his Lovecraftian terror aura on while still in human form - it does wonders for negotiations.
If he had just been a simple mafioso, those gathered there would not have felt such an alien sense of awe. The aura rolling off of him was that of innumerable things mixed chaotically together... of something that was not human.
Doctor Manhattan of Watchmen fame shows signs of becoming this throughout the story due to his growing detachment from, well, everything. He ultimately embraces humanity, sort of, but not his own. At best you could say he recognizes the value of humanity. What he actually does is to go off to a galaxy far, far away to play God.
The Shade looks and acts human enough (though some artists do portray him with a certain pallor), but his powers are taken straight from the fabric of a dimension holding a godlike Eldritch Abomination and have essentially become one with him, making him ageless and virtually unkillable, not to mention terrifyingly powerful. Thankfully for us, he's generally a fairly nice guy (not a hero by any means, but definitely not an outright villain either) and is perfectly willing to leave you be... that is, unless you attempt to attack Opal City. In that case, all bets are off.
Mad Jim Jaspers of Captain Britain crosses into this realm thanks to his abilities being strong enough to make him nigh-omnipotent, with it being heavily implied that he exists partially in a metaphysical realm, as well. He's so powerful that his entire continuity had to be destroyed to prevent it from becoming infectious and warping reality in other continuities. Earth-616 also has Jaspers, and he's even more powerful. It took an invincible, infinitely adaptable killing machine that the original Jaspers created and that escaped from the destroyed continuity to bring the 616 Jaspers down. It transported him to a reality-free area to deprive him of fuel for his abilities. The resulting toll on the being was so great that he was put down without much difficulty by Captain UK.
The Moonchild/Antichrist from The League of Extraordinary Gentlemen is a bald man that can grow into gigantic heights with eyes all over his body. He progressively looks worse as the heroes try to hack him apart, rendering him a fleshy pile that quickly regenerates into his original form. He also happens to be Harry Potter.
Abraxas looks like a human with green skin who wears a toga, and he makes Galactus seem positively cuddly in comparison. Indeed, one of the reasons Galactus even exists is to keep Abraxas in check. Abraxas is the opposite of Eternity, who is the Anthropomorphic Personification of well, eternity, making Abraxas the ultimate embodiment of unfettered destruction in the Marvel multiverse. Abraxas is fully willing and capable of killing entire universes, and the only way to get rid of him other than by reviving Galactus is to destroy all reality.
Psyko, the warped Evil Counterpart to Sleepwalker was originally human before he was exposed to a wave of perverted demonic energy from the Mindscape. It completely fried the brains of every other human in the area, but he simply absorbed it and turned into a humanoid... thing with bone-white skin, a skull-like face, bone-like spikes growing out of his body, insane glowing eyes, and teeth as long as a man's finger.
Yuuka Kazami in the Touhou fanfiction Imperfect Metamorphosis is horrifically powerful, inspires petrifying dread by her very presence, not even Yukari knows what the hell she is (and notes that her powers are disturbingly ineffective against her), and even with the Shadow Youkai running around and causing a mess of everything nearly everyone treats her as the bigger threat. Later events reveal she's actually an Outer God, straight out of Lovecraft.
While his true morals or intention is open to interpretation, the "Mystery Man" in David Lynch's Lost Highway can certainly come off as this to a first time viewer. The extensive make-up that covers his eyebrows and makes him inhumanly pale and the camera's tendency to get uncomfortably close to his face during his scenes certainly doesn't help.
From the Phantasm franchise, The Tall Man is perhaps one of the best known examples of this on film. He looks like an old man in a suit, albeit an intimidating one, but is really implied to be some horrible otherdimensional conciousness wearing the form of a man named Jebadaiah Morningstar like a meat suit. He bleeds a milky white fluid when injured and his fingers have been known to turn into hideous bug-things when severed. He is hideously strong, controls an army of deadly silver spheres, and even has some Reality Warper powers. He has a nasty agenda that involves killing people and turning them into twisted dwarfish slaves to use in another dimension.
"Everyone who saw her at the police court said she was at once the most beautiful woman and the most repulsive they had ever set eyes on. I have spoken to a man who saw her, and I assure you he positively shuddered as he tried to describe the woman, but he couldn't tell why."
In The Light Fantastic, everyone expects the Things From The Dungeon Dimensions to come storming into our reality with tentacles waving, but all they need is one mind. And when Rincewind looks into Trymon's eyes, it's every bit as horrific as anything involving tentacles and Alien Geometries.
I Shall Wear Midnight introduces the Cunning Man, the shade of a fanatic witch-hunter who was so obsessed he went on even after eventually having no body. He appears as a man in black with empty holes for eyes (no, not empty eye sockets, HOLES, you can see through them) and Invisible to Normals; to those who can perceive it, he also appears to exude a terrible stench, though rather than an actual physical stench this is their mind's perception of the corruption in his. He can use mirrors, pictures and the like to enter the world, and can possess the bodies of others. To hammer home how utterly wrong he is, it should be noted that, in Discworld, the eyes always show a person's true nature. Even the gods can change anything about their appearance except their eyes. Now the Cunning Man has nothing there, as in seeing into the front and out the back of his head.
The Beast, AKA Martin Chatwin from The Magicians is mistaken for an Eldritch Abomination at first, but during the climactic battle, his Evil Gloating reveals that, as a boy, he escaped into the fringes of the Fillory world and accepted the darker magic of its inhabitants wholeheartedly, transforming him into a god-level power. The result is not pretty◊
Cassandra, the antagonist of Full Tilt, appears as a young woman with red hair and blue eyes. It's made apparent almost immediately that she's very old and very powerful, and that she created the supernaturalAmusement Park of Doom in which most of the story is spent. However, she tends to either influence things from a distance, or get involved through use of weaponry rather than magic—her only direct demonstration of her true nature is a Stealth Hi/Bye.
According to Star Wars Expanded Universe, Palpatine was one of these as well before being Killed Off for Real. He had delved so far into Sith lore and power that he became more or less an embodiment of the Dark Side itself. He had to keep cloning himself new bodies since his own dark powers kept consuming them.
This seems to happen from time to time to Sith who immerse themselves fully in The Dark Side.
The Shrike in Dan Simmons' Hyperion Cantos is a ten foot tall, four armed razor covered thing that can manipulate time and indiscriminately kills anyone who gets too near the "Time Tombs" on the titular planet.
The Clockmaker, from Alastair Reynolds' The Prefect. Can assume any shape, but its default form resembles a stretched out human form, spindly and quicksilver. Enjoys wanton slaughter and leaving intricately designed clocks and trinkets around... which may or may not be Body Horror-inducing booby traps.
Angleton, AKA the Eater of Souls in Charles Stross' The Laundry Series is eventually revealed to be this. Subverted in that he's undeniably one of the good guys, even if he lives in the Uncanny Valley and therefore frightens the hell out of his subordinates. What happened was that he was summoned and bound in the 1930s, taught to pass for human, and eventually Humanity Ensues. Strangely, it's implied that he believes in decency and fairness more than the people around him—he's not averse to pulling a few strings for Bob and Mo's sake.
All over the place in The Dresden Files. There's the two Faerie Queens, Mab and Titania, who are unfathomable even by fae standards, the Lords of the Outer Night in the Red Court, and Shagnasty the Skinwalker. Then there are the Faerie "mothers", who are an order of magnitude more powerful than the queens. Some Outsiders can also take humanoid form, such as "Sharkface" in Cold Days.
The Myrddraal from the The Wheel of Time are comparatively minor examples, but they still qualify. Born among the Trollocs, they're a throwback to the Trollocs' human heritage, but warped by the Black Magic that created them- they resemble eerily pale, graceful humans except that they have smooth skin where eyes should be and have a number of bizarre abilities that cannot be explained by the series' main magic system. They're also absolutely devoid of emotion except for cold-blooded sadism and are all completely identical in terms of appearance and personality. Even human villains who encounter them are prone to remark on how unnatural they are.
And there is Shaidar Haran, a Myrddraal that acts as the Dark One's avatar, and later an incubator of sorts.
And Padan Fain, who starts out as human, but through a convuluted series of misfortunes, becomes the living embodiment of another evil power, possibly as bad as the Dark One.
Most of the plot in Graeme Penman's Motherland revolves around the villain trying very hard to become a Humanoid Abomination as opposed to the malevolent cloud that he is at the moment.
"I suppose you could call them men, yes. Two legs, two arms, a head each."
The Endlords from Sword Of Shadows look like tall humans in dark armor, but it's made quite plain that they are in fact cosmic forces of destruction which have been compressed into this shape, and are utterly inimical to life as we know it.
Illyria's original form was a massive tentacled creature; she's an Old One, a shout-out to HP Lovecraft. But since she's stolen Winifred Burkle's body, we mostly see her looking like a blue version of Fred.
Jasmine. The most we could get from her true form was a shadowed mass of tentacles and is mentioned by her abandoned demon followers as the "Blessed Devourer." Those who are immune to her mind-control charms don't see her as a beautiful woman but a corpse filled with maggots, and her true name cannot be pronounced by human words (Angel needed a stitched up demon follower because it was the only thing capable of saying her name and breaking the spell).
Buffy the Vampire Slayer had one of these as its Season Five Big Bad. Glorificus, aka Glory, was an exiled hellgod that was reduced to using a hapless human host as a timeshare. Whenever Glory takes control of its (male) host, it looks like a glamorous woman. Even in this form Glory is a Nigh Invulnerablesuperstrong menace that can rob people of their sanity and eat it.
The Time Lords at the end of the Second War in Heaven and the Last Great Time War have continued to regenerate into forms that are ideal for waging chronological war - in the first case, war against what can only be approximately described as a sapient timeline. Guess what this implies for ordinary Time Lords?
The new series plays with this possibility often. The entire sixth season was based around a conspiracy to kill the Doctor because apparently simply speaking his True Name would end the universe.
Consider this description of the being the Pandorica was designed to hold: "A nameless, terrible thing, soaked in the blood of a billion galaxies. The most feared being in all the cosmos. And nothing could stop it, or hold it, or reason with it. One day it would just drop out of the sky and tear down your world." It's the Doctor.
In "The Family of Blood", when "John Smith", the Doctor's temporarily human persona, is told of his true identity and given a description of what the Doctor is like, it completely scares the hell out of him;
Tim Latimer: He's like fire and ice and rage. He's like the night and the storm in the heart of the sun...
"John Smith": *Quietly* Stop it.
Tim Latimer: He's ancient and forever. He burns at the centre of time and can see the turn of the universe...
"John Smith": *Panicking* Stop it, I said stop it!
The Celestial Toymaker, in the original series serial of the same name, resembles a middle-aged Caucasian man dressed in Mandarin robes who engages in silly, over-sized versions of board games and toys. He however controls his own universe and has vast powers over time and space. In one Expanded Universe novel, he is depicted more horribly and is outright stated to be using the powers of the Great Old Ones.
Also in the Expanded Universe, humanoid TARDISes... it's mentioned as being especially creepy when they open to take on passengers.
Maryann Forrester. Even other supernaturals have no idea what she is, only that she's incredibly powerful, with viscous black blood that is poisonous to vampires and immunity to all supernatural and conventional forms of attack. She drives her followers to wild, hedonistic behavior, complete with the requisite Human Sacrifice. She is eventually identified as a Maenad, a female follower of Dionysus, but the explanation of what type of creature a Maenad is in this setting is suspiciously vague. One of her followers claims Maryann has been alive as long as there's been an Earth to walk on and was known in ancient times as the demon Lilith and the goddesses Gaia and Isis.
The Biblical demon Lilith herself, who appears in the form of a young woman made entirely of blood (or alternatively just naked). Her very presence causes all vampires in the immediate vicinity to give into their darker, bestial impulses, even those with the most self-control, she communicates via piercing screeches, and consuming enough of her blood is enough to transform the drinker into something very much like her, if not her physical avatar on Earth. Just ask Bill.
LOST gives us the Man in Black, a post-human entity who takes the appearance of deceased individuals when not being a cloud of black smoke.
Kenneth in 30 Rock. Oddly, he combines this with being The Pollyanna. See his first words, said the day he was born.
Momma, I am not a person. My body's just a flesh vessel for an immortal being whose name, if you heard it, you would lose your mind.
In Luca Turilli's Prophet of the Last Eclipse this seems to be the case with those touched by the Black Portal. They appear perfectly human, but demons (which can literally never die and may very well be true abominations in their own right) are instinctively terrified of them. And spilling the blood of one can result in The End of the World as We Know It.
Imaginos, the central figure of the Blue Öyster Cult album of the same name, is most definitely this. Admittedly, prior to being 'recruited' by Les Invisibles he was more 'humanoid' since he apparently thought of himself as human despite being a psychic shapeshifter, but afterwards he became more of a 'abomination' and is downright gleeful about it.
Marilyn Manson's concept album Antichrist Superstar has, well, the Antichrist Superstar, the reality-destroying result of The Worm becoming fed up with his sycophantic followers. While his appearance was unknown, the finished-but-unreleased video for Antichrist Superstar was leaked almost a decade later, which does show him in this form. If the Grim Reaper had sex with a fallen angel and they somehow had a kid, it would be an apt description.
Mythology and Religion
If you look at urban myth, The Grinning Man, the Moth Man, Springheeled Jack, the Cornish Owlman, La Llorona, Black-Eyed Kids, heck, quite a lot of urban myths or cryptid sighting run on this trope. Many of these things might actually be resulted from encounters with owls, specially barn owls, which they frequently resemble with the massive eyes and wing-like arms. Owls themselves, much like some other birds, do look vaguely humanoid, being erect bipeds, which is part of why they're frequently considered unnerving.
Nyx, personification of Night from Classical Mythology. Usually represented as a beautiful female human, yet a quick look at her children - most of which she gave birth to by herself alone - should tell you what kind of being she really is. If that doesn't convince you yet, the fact that even Zeus fears her should.
Cú Chulainn, the young hero of the Ulster Cycle of Celtic Mythology, particularly of the Táin Bó Cúailnge. Though he is portrayed as being as Bishōnen as a teenaged Irish ginger can be, he is a descendant from the Fomorians, a monstrous race from the mythic prehistory era of Ireland. Though he is heroic and stalwart, and generally perceived as a good guy, his defining mystical characteristic is his ability to transform into various disfigured superpowered abominations through the use of his warp-spasm. After he transforms, he becomes a berserker that slaughters anything in his path, friend and foe alike.
Some of the angels in Abrahamic religions, such as Christianity and Judaism. It is clear that some angels like Gabriel can appear as humanoid, but their real forms are at best highly confusing and at worst mind-numbingly horrifying. And they're not even alive anyway, as their entry on Eldritch Abomination shows. Note that only some bother to appear as humanoid however, as many in The Bible and the Qu'ran don't even bother to disguise their real forms.
Daniel saw an angel that was invisible to everyone else, carried with it an aura of fear, and had a glowing face (like lightning) and eyes of flame. Also a body carved from gemstones.
According to one interpretation, a lot of the angels mentioned early on in the Bible (especially in B'reshit/Genesis) are in essence the will of God made manifest in temporary human form. So while they're described as men in the text, they really really aren't.
Satan is described as "appearing in the guise of a young man."
The angel of the lord itself is described as a man who was "terrifying to look at" by Samson's mother and when Samson's father asked its name he replied "You wouldn't understand if I told you." Despite or perhaps because of this, apocryphal works call him Metatron which basically means "less than four the letter word" (Tetragrammaton, a title for God).
Atropals from Epic-level DnD, the stillborn fetuses of Gods, also capable of shedding smaller Atropal Scions. Unsurprisingly, they are as terrifying, powerful and hideous as the description suggests.
Elan look (and used to be) human, but their strange creation ceremony... changes them. In game mechanics terms they don't count as Humanoid (Human, elf, goblin etc.) or even Monstrous Humanoid (Minotaurs, medusas), but as Aberrations. In DnD, aberration are explicitly eldritch horrors. And this can be done to you against your will. As a bonus, this grants them immunity to many common spells that only work on humanoids, such as the famous and powerful Hold Person.
Like the Elan, humanoid races can also become Aberrations via the Fleshwarper Prestige Class. They're capable of creating temporary implants for others, as well as permanent traits for themselves, until eventually they become a full Aberration themselves. Incidentally, the class's only restrictions relate to Law and not morality, and most are simply eccentric. The psion prestige class that lets you become more and more like a Mind Flayer, on the other hand, tends to be for amoral assholes only.
There is also the alienist arcane Prestige Class, which makes you more and more in tune with the Far Realm; by the time you finish the progression the only thing humanoid about you is your body's shape, for the most part.
Daelkyr from Eberron, high-level outsiders from the plane of madness. Notable in that they looked like this when they invaded the main continent ages prior, before humans had ever set foot there. When human explorers did arrive, later, they created a panic among the demihuman populace due to the resemblance. Keith Baker, creator of Eberron, was once asked why daelkyr looked so much like humans. His response was that the real question is why do humans look so much like daelkyr...
Mage The Awakening has "the Other," the Astral Aeon of the Abyss, who is said to look simply like an unassuming, shrunken, slightly odd old man, who nevertheless has something indescribably off with everything about him.
Similarly, each of the True Fae from Changeling The Lost has a humanoid Mask that they can wear when they appear on Earth. These masks can be beautiful or hideous, but usually within the realm of human expectation... except for the one element that's just wrong.
This is also what most mages think of geniuses — that they are bizarre cosmic intelligences of unknown motivation and origins who simply look human. In the case of the Illuminated, they may well be right. The "inverted Geniuses" known as Clockstoppers may also be examples — one of the most powerful is described as being more a force of nature than a man.
Old World Of Darkness has the Onceborn of Wraith The Oblivion, effectively dead gods in service of the necrotic force known as Oblivion. Unlike their cohorts, the Neverborn, they were human at one point... but they were such bastards in life, they plummeted right into becoming Spectres upon death, and then ascended to the ranks of horrible divinity.
The Yozis and their varioussouls can appear in any number of bizarre, logic-defying forms, including entire living worlds... or they can appear as inhumanly attractive humanoid beings with a few thematic characteristics here and there. They can also do both at the same time — all demons above the First Circle have the ability to manifest in multiple locations at once. The Primordials Gaia and Autochthon are just as eldritch, except they haven't been mutilated and imprisoned in Hell. Gaia's most familiar form is a beautiful humanoid goddess who hangs out in Heaven.
The Fair Folk qualify, being even more monstrous and alien in this setting than is standard for that trope — they come from what is essentially an alien universe characterized by having no laws of physics, they have no actual personalities or motives, and they can only exist in Creation by eating human souls. Yet, as far as appearance goes, many of the Raksha nobles are inhuman only in their extreme beauty. It helps attract prey, you see.
According to Word of Sol, the Green Sun Princes qualify to a degree, having taken the Yozi nature into their once-human souls, and are gradually evolving into Yozi-like beings.
In a way, all of the Exalted are this. Human beings were never meant to receive power in the manner of the Exalted, and elder Exalts tend to have viewpoints that are rather skewed for one reason or another. They can also easily be impossibly beautiful.
The Immortal God Emperor of Mankind. Long ago, all of Earth's mages, psykers, and mystics decided that humanity needed a champion to lead them. They committed mass suicide and all of them were reincarnated as one being: the Emperor. Anyone who had the misfortune to make psychic contact with him and got a glimpse of what lay beneath the surface, such as John Grammaticus (a powerful psyker in his own right), would be left in a state of total awe and terror — mostly terror. The making of Astropaths even uses this deliberately, the aspiring Astropath making contact with the (severely weakened, maybe dead) Emperor for a brief instant, with the delightful effect of being able to transmit signals across the galaxy as well as having their eyes burned from their sockets.
Horus became one of these at the end of the Horus Heresy, with all four of the Chaos gods using him as a vessel of their power at once. The battle between him and the Emperor left him dead and the Emperor mortally wounded.
The final stage of R-Type Delta features human fetuses floating around inside of crystalline structures, giant killer sperm, giant strands of DNA, and giant fertilized eggs, all floating around in a starry void populated with floating Earth buildings and other memories of mankind's achievements and all trying to murder you dead. The "true" final stage of R-Type Final seems to feature silhouettes of a male and female human in coitus in the background. R-Type is quite literally fucked up.
Most Final FantasyBig Bads pass through this at some stage of their life cycle. They almost all pass out of it later when powering up, advancing to more conventional abominations, of course, but the intermediate stages still qualify.
Exdeath is actually an aggregate of evil souls trapped in a tree, but spends most of the game as a humanoid suit of armor. How he managed to fit a classic Eldritch Abomination appearance like his into a suit of armor small and human enough to deceive people isn't known, but he isa wizard.
Ultimecia managed to destroy time itself but still exists quite comfortably and is a Sorceress, something not quite human but looking the same, until the final boss fight; she loses the "humanoid" part when she shifts from "break the universe" mode into "break the skulls of the impudent mortals before me" mode.
Yu Yevon was once human, but turned into a jellyfish-summon-disease-thing using the only powers available to him as a human and instead simply wears an actual Eldritch Abomination as a suit of armour. He counted back in the day when he made the first Sin, though, and might have counted longer depending. We don't really know the how or why of his current blobby appearance, so it might have been a gradual thing.
Blue Mages also become these after accepting a shady offer of power - it is implied they become even moreso as they devour monsters' magic, and those who don't control themselves can cross the line into a Soul Flayer.
Vayne Solidor started out as an ordinary Hume, albeit one who knew kung fu. Then the godlike Occuria Venat, out of gratitude for Vayne's help in fulfilling her Evil Plan, merged with him so that he would not face death alone. This fusion became The Undying, a humanoid monstrosity with pieces of Vayne's sky fortress attached to it that gave it the appearance of a mecha-angel.
In Final Fantasy Tactics Advance, the final boss is an inscrutable genie-thing that preys off of insecurities... and spends most of the game looking like the dead mother of one of the characters.
Organization XIII from Kingdom Hearts II. Like the rest of their Nobody brethren, their semi-existence is so unnatural, so deeply wrong that even the darkness rejects them. Unlike the others, however, they look exactly like humans with odd powers.
On that note, most Nobodies resemble humans in shape. All they are in reality are stretchy rag dolls who apparently have taken combat lessons from Voldo.
Special mention goes to Xion for not actually being a Nobody. That's right, even the Nobodies rejected her.
Kingdom Hearts like these; the first game features Ansem, or rather, Xehanort's Heartless, who is a humanoid Heartless and the prequel has Vanitas, a being made from another character's Darkness and is the original Unversed and origin of every Unversed you fight in the game.
Drakengard has the Grotesqueries, gigantic, sharp-toothed babies capable of taking on godlike dragons and who enjoy the taste of flesh, who fall down from the sky on wings of lightning when you kill the Big Bad. In the sequel, you learn that those are literally that world's GODS, the same ones who controlled said Big Bad. That kind of octane factor's for premium fuel only.
Certainly there's Nuurag-Vaarn, the Chaos Archmage, who is the penultimate Boss Fight for the normal ending. He appears as a withered old man whose eyes are holes radiating such unbearable light of power you can barely catch a glimpse of the tentacles writhing in them. (Well, actually he appears as a "@" but this is what the description says.)
There's also the Big Bad, who's so incomprehensible that the game bluntly says he's beyond description.
Heretic: Aside from the fact that we never see his face, or body for that matter, there's nothing visibly inhuman about D'Sparil's appearance, even though he's a demon that slipped in through a hole in the walls of the cosmos from the outside. He makes up for this by riding a humanoid serpent with an appropriately eldritch appearance.
The Heresiarch from Hexen, a near-unique boss creature, is an immensely powerful magic-using humanoid creature of some sort. Most of its appearance is hidden inside its robes, like D'Sparil's, but claws and a tail can be seen at the bottom. It's a leader of the cult of the Serpent Riders, but there isn't really much of an indication what it actually is, aside from something eldritch and unnatural.
D'Sparil's older brother Eidolon from Hexen II is a humanoid, though a demonic-looking one.
Lavos from Chrono Trigger. At its core, beyond all its protective layers, it resembles nothing more than a (comparatively) small humanoid alien astronaut. It is also its most hideously powerful form, whose mere presences distorts time and space. And it's not even Lavos's real body anyways.
Alma, as she grows in power, may be evolving from Stringy-Haired Ghost Girl to full-blown world-threatening abomination, yet so far seems to have kept her somewhat human looks.
There's also the Creep in the third game: though humanoid, it is far more monstrous and aggressive than Alma. It eventually turns out that it is an amalgam of the worst memories Fettel, the Point Man, and Alma have of Harlan Wade, given life by Alma's psychic powers.
The Tall Man from the Chzo Mythos, Prince and servant of the pain elemental Chzo. Very prominent in the midquel game Trilby's Notes, where he manifests in the shifted world as a bone white androgynous figure with unnaturally long limbs and a black longcoat. Though this is probably because he used to be human until Chzo took over him.
Xerath, a mage of an ancient culture who ascended to a higher plane of existence; Fiddlesticks, an extradimensional being trapped in a scarecrow; Brand, an apocalyptic spirit of fire possessing a man; and Nautilus, an abyssal, deep-sea entity inhabiting a man and the dive-suit he wears.
Of special note are also Kassadin and Malzahar, both of whom have been touched by the Void, an extradimensional space where Lovecraftian creatures lurk. Both wield Void magics, but with very different goals. Whether anything human actually remains of them is debatable.
In Vagrant Story, anyone who bears the Blood-Sin Tattoo which grants its bearer access to the power and knowledge of the Gran Grimoire, the ultimate codex of magic that takes the form of an entire city, becomes a fearsome immortal magical being while still looking like a normal human. Though Romeo Guildenstern is somewhat mutated when he eventually acquires it and does eventually go One-Winged Angel.
The GMan of Half-Life... Maybe. To be certain, he's dead center in the unnerving category, has scarily thorough, though unknown amounts of knowledge of the protagonist and events, and displays powers that are magnitudes beyond anything else in the series (it required the entire Vortigaunt race working together just to stall him, and even that didn't last long). And he says he reports to a higher power. There's a good reason a lot of fans compare him to Nyarlathotep.
True Zenon from Disgaea 2 also qualifies, as does series Bonus Boss Baal. Both of them, while shaped like people usually, are utterly inhuman mentally even compared to other demons, are strong enough to slaughter overlords by the hundreds, and even go Body Surfing when the need arises, almost always to another deceptively human vessel. Almost being the key word; Baal, having had to surf more often, has worn a few low-level mooks in his time.
As of Sengoku Basara 3, Oichi is, if not one outright, at least on her way to becoming one. She's been robbed of the last shred of her sanity, seeing the world through a bizarre, alien dream logic, and is simultaneously the master and puppet of the dark powers she showed in the previous game. She gets better in some of her endings.
Deadly Premonition has Forrest Kaysen, who he is revealed to be a dimension-warping abomination. He certainly isn't as indestructible as the average Humanoid Abomination though, as Francis Zach Morgan is able to dismissively murder the son of a bitch with a well placed bullet to the brain.
According to Word Of GodWillie is Kaysen's overseer, delivering his instructions from the Red World.
Shadow of the Colossus has almost no exposition and very little dialog, and as all characters already know why they have come to the place, they don't talk about it and leave the player almost completely in the dark as to what's really going on. Dormin is actually quite nice when they talk to Wander, but the fact that they have been sealed in the temple and the way the pursuers in the last quarter of the game react to the place make it quite apparent that they are regarded as a kind of eldritch abomination by the people.
The final boss, Satan himself, appears simply as a tall man with long black hair and shining, amber eyes. He appears nude, but there's a veil of shadow clouding his waist.
The Lords of Shadow also qualify before going One-Winged Angel. The three Lords of Shadow are actually the bodies of the founders of the Order that are animated by the evil that they left behind when they ascended to Heaven instead of souls. Cornell and Carmilla have some inhuman characteristics but still look fairly human. Zobek on the other hand looks completely human before transforming.
From the main series, we have Dracula himself. Far more than just a vampire, he is revealed in Dawn of Sorrow to be a fundamental force of the universe necessary for maintaining the Balance Between Good and Evil, and his role is literally to be the opposite of God.
The Outer Space Beings from the Sin And Punishment series are from outside the universe as we know it, have strange and immense powers, have blood that can grant people special powers, are implied to be the source of many of the bizarre lifeforms found in the series... and can look perfectly human. The fluff reveals they can look like anything they want. And Achi, Big Bad of the first game, shapeshifts into a planet for the final boss fight.
Some of the Daedric Princes in The Elder Scrolls manifest themselves as humanoids, some more normal looking than others. Perhaps the most normal-looking is, bizarrely enough, Sheogorath, the Prince of Madness. At first glance he looks less like the physical avatar of insanity and more like a grandfatherly banker you'd trust right away. This is, of course, entirely the point.
Dead Space 2 has Nicole. While she is just a hallucination, she's still a monstrous personification of Issac's guilt over failing to save the real Nicole, and a projection of the gigantic Artifact of Doom Isaac inadvertently helped build.
Minecraft has the "Enderman" mob, which is based off of Slender Man. They're three-meter-tall, completely black humanoids with glowing eyes. They wander around at night, and unlike other monsters that actively search for you, endermen ignore you as long as you ignore them. However, if you look directly at them, they turn to stare at you, then attack as soon as you break your gaze. They can teleport to get closer to you, and to dodge arrows. They run quickly at you when you can't see them. When you look back at them, they stop moving and stare at you, with their mouths opening and shaking violently. They're the only mob able to pick up blocks. In a recent update, they've gained a few extra sounds they can make, including a long, rising, unearthly growl that seems to come from nowhere in particular. It was eventually revealed that they're aliens from another dimension called The End, and you need to travel to their homeworld to beat the game (insofar as you can ever "win" a Wide Open Sandbox with no plot).
Pyron from Darkstalkers is an ageless energy being who exists solely to drain planets like a vampire. Hideously powerful, he spared Earth millions of years ago solely because he wanted to wait until it got tastier. His preferred form is a flaming humanoid, though he demonstrates complete control over his form. The scary part? Pyron isn't a standalone monstrosity. He's just another member of his race. There's an entire planet of these things. He does get his ass kicked by the other Darkstalkers, many of whom could qualify for this trope in their own right.
Dishonored has the Outsider, an...entity that seems to have existed throughout the whole of recorded history - and before. You'd mistake him for a handsome young man in plain clothing were it not for his totally black eyeballs, his tendency to be wreathed in shadow, and that he seems to enjoy hovering a foot or so off the ground. His hobbies include speaking with polite bemusement about mortal affairs, entering people's dreams to inspire bizarre inventions, branding those he deems "interesting" with his mark to grant them really weird powers, being alternately worshipped as a god and vilified as a Satanic figure, and hanging out in a realm called The Void which may or may not be slowly consuming reality as its inhabitants know it. Anecdotal evidence suggests that he may be using A Form You Are Comfortable With, and he's actually a Space Whale...which in the Dishonored universe, means he's pretty Lovecraftian in his appearance (though far from Go Mad From The Revelation levels).
OFFwill catch you by surprise with one of these, depending on the Alternate Ending you pick. It helps that the thing's on the very edge between this and a full-blown eldritch in appearance, and that from your perspective, it had you fooled the entire time.
Dark Samus, the main antagonist of the Metroid Prime trilogy, resembles a black, biomechanical version of Samus Aran. "She" began as the titular Metroid Prime, a Metroid mutated by prolonged exposure to Phazon and prophesied by the Chozo as the Worm. Following Metroid Prime's defeat at the hands of Samus, it merged with her Phazon Suit and came back as a twisted doppelganger bent on spreading Phazon throughout the universe and even other dimensions, and was unkillable as long as Phazon existed.
Amnesia The Dark Descent: The Big Bad, Baron Alexander von Brennenburg, is eventually revealed to be a being from another universe that got exiled into our own. He takes a human form to fit in with our society, but as the game goes on it's clear he is something else. Looking at a portrait of him while low on sanity transforms his face into a horrific corpse-like visage, which is believed by some to be a glimpse at his true form.
Subtly implied with Gardevoir in the Pokemon series. Despite looking, well, human-like, it's not in the "human-like" breeding group. It is in fact in the "Amorphous" group, which means it can breed with things like Weezing, Muk, most Ghost types and a giant electric lamprey. It's also the only thing in its egg group that really looks like it doesn't belong there. All that Rule34 suddenly got a whole lot Squickier.
Tsukihime has Nero Chaos, who has a body composed of hundreds of animals that can detach from him to attack and feed. Even his mind is a gestalt, and his original personality is slowly being subsumed into the collective consciousness.
Rithuly from Sluggy Freelance, a vaguely defined "dark god" with strong Eldritch Abomination vibes: his "true form is of a great flying Stygian dragon" but he "usually appears man-sized, either as a wispy tentacle-headed dark ghost or a charming handsome man in a white robe adorned with jewelry."
A look into her past reveals that Jones qualifies. Her existence predates life on Earth by at least a few billion years, but she has always looked the same. She has a perfect memory for every instant of her entire history, scratches diamonds, and is impenetrable to x-rays. She claims to lack emotions or imagination; though Antimony has her doubts on this matter, it might just be projection on her (and the readership's) part. Oh, and she has no idea what she is, either. MYSTERY SOLVED!
Ow My Sanity has tons of these, many of which are female. The kicker? They're the protagonist's Unwanted Harem, which has strange implications for just how much more of a Deconstruction the series is going to become.
Jack Noir has become this as well after he prototyped with Bec. Even Doc Scratch says he's stronger than him now.
And after learning the answer to a certain question, Rose at least partially turns into one too. She's got grey skin, is surrounded by black magic, and can only speak in Black Speech. She's also gone a little crazy. However, she still seems to have the same personality and care about her friends. She later returns to normal after she dies and is revived as her dreamself.
The Slender Man, pictured above. You can just about mistake him for a human being at a distance (unless he's in full-on Combat Tentacles mode), but come any closer and you start to... noticethings. Marble Hornets, one of the most famous Slendy stories, is an excellent portrayal of this trope. The Slender Man distorts reality just by existing, driving some characters into homicidal madness. He seems to have a goal of some sort, but whatever it is, it's utterly inscrutable.
Another well-known creepypasta creation, The Rake, also counts. A freakish hairless dog-man who seems to have similar stalking habits to Slenderman, albeit being more direct with his victims*
Slendy watches from a distance; the Rake likes to sit on your bed. While you're in it
. Has even showed up in Everyman HYBRID, integrating it into the above mythos.
The SCP Foundation has absolutely every type of abomination, and these are no exception. There's some creepyReality Warpers hanging around there.
Dr. Clef claims to be one himself: he discovered what he was at an early age when an idle thought caused the Challenger disaster. He then devoted his life to putting the kibosh on those more selfishly inclined than he. This is still Clef, though, so take it with a mine of salt.
Creepy Child SCP-053 looks and acts like an ordinary three year old girl. She's not. Let's put it this way: SCP-682, an alien reptillian Omnicidal Maniac that hates everything in this universe on principle, likes SCP-053, and the feeling is mutual — once SCP-053 got past her initial fear of the giant terrifying reptiloid. (It's kind of adorable, actually.)
Along the lines of the Slender Man, SCP-582 appears and acts out his part in any stories written about him.
Ace in Ruby Quest, a silent, masked Implacable Man who appears to be central to the mysteries surrounding the facility and may or may not be The Worm That Walks. Additionally, all of the normal people in the facility are either on their way here or past it and heading towards pure, concentrated Body Horror.
Atop The Fourth Wall: The Entity/Missingno can apparently only manifest itself in the physical realm by taking the form of another.
Breach qualifies. She's a Creepy Child with extra arms, one set oversized, and creates portals. She keeps people as playthings in her pocket dimension.
Miss Bitters from Invader Zim. Nobody is exactly sure what she is, but human is not on the list of options. She is implied to be older than the Skool (they couldn't make her move so they built it around her and made her a teacher) and has taught at least two generations worth of students. The official website mentions rumors state that she is the spawn of an English teacher and a really big snake. Her flashbacks in the series indicate she was once much happier...
Wall-Mart in the South Park episode "Something Wall-Mart This Way Comes". Wall-Mart is actually portrayed as a complete Eldritch Abomination in the episode, being an abstract entity from beyond that exists as long as there is consumerism and poisons every town in which it manifests itself. Near the end of the episode however, it temporarily takes on human form so it can talk to Stan and Kyle.